Mahalanobis Distance

[cdueben]

transition() produces an error in the RasterBrick case.

x <- raster(matrix(data = c(15, 20, 7, 12, 13, 18, 6, 5, 1, 21, 3, 15, 22, 17, 12, 14), nrow = 4, ncol = 4, byrow = T))
y <- raster(matrix(data = c(690, 623, 673, 442, 750, 620, 680, 491, 467, 489, 624, 590, 552, 605, 727, 462), nrow = 4, ncol = 4, byrow = T))
x <- brick(x, y)
z <- transition(x, transitionFunction = "mahal", directions = 8)
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'nrow': error in evaluating the argument 'x' in selecting a method for function 'transitionMatrix': invalid class “TransitionData” object: FALSE

It is linked to line 324 in transition.R.

directions <- 8
x <- raster(matrix(data = c(15, 20, 7, 12, 13, 18, 6, 5, 1, 21, 3, 15, 22, 17, 12, 14), nrow = 4, ncol = 4, byrow = T))
y <- raster(matrix(data = c(690, 623, 673, 442, 750, 620, 680, 491, 467, 489, 624, 590, 552, 605, 727, 462), nrow = 4, ncol = 4, byrow = T))
x <- brick(x, y)
xy <- cbind(1:ncell(x),getValues(x))
xy <- na.omit(xy)
dataCells <- xy[,1]
adj <- adjacent(x, cells=dataCells, pairs=TRUE, target=dataCells, directions=directions)
x.minus.y <- raster::getValues(x)[adj[,1],] - raster::getValues(x)[adj[,2],]
cov.inv <- solve(cov(xy[,-1]))
mahaldistance <- apply(x.minus.y,1,function(x){sqrt((x%*%cov.inv)%*%x)})
mahaldistance <- mean(mahaldistance)/(mahaldistance+mean(mahaldistance))
transitiondsC <- new("dsCMatrix", p = as.integer(rep(0,ncell(x)+1)), Dim = as.integer(c(ncell(x),ncell(x))), Dimnames = list(as.character(1:ncell(x)),as.character(1:ncell(x))))
transitiondsC[adj] <- mahaldistance
tr <- new("TransitionLayer", nrows=as.integer(nrow(x)), ncols=as.integer(ncol(x)), extent = extent(x), crs=projection(x, asText=FALSE), matrixValues="conductance", transitionMatrix = transitiondsC)
Error in h(simpleError(msg, call)) :
  error in evaluating the argument 'x' in selecting a method for function 'nrow': error in evaluating the argument 'x' in selecting a method for function 'transitionMatrix': invalid class “TransitionData” object: FALSE

Do you know how to fix this?

[kauedesousa]

Thanks @ChristianDueben I am trying to figure out how to solve this issue. It may be also related with the exports on the latest version when we moved the code to roxygen2. I will check the previous versions and get back to you.

[JamesWGriffiths]

Hi, I have run into the same issue as @ChristianDueben with transitionFunction = "mahal". Has a fix been identified?

[scbrown86]

This issue is still occurring. Are there any plans to fix this function?

[Rilquer]

Hello, all.

Just wanted to say I am getting a similar error with transitionFunction = "mahal" on a RasterBrick of 19 bioclimatic variables. Was wondering if this error was fixed.